Bio-Tools-CodonOptTable
A codon quality check tool, it produces a Codon Optimization table to see the quality of each codon.
The simplest way of depiction is to plot the codon usage frequency that can be found in common codon usage tables. A more elaborate way to depict the codon quality is to convert the codon usage frequency into relative adaptiveness values. In contrast to the codon usage frequency the relative adaptiveness takes into account the number of codons which code for the respective amino acid.
We produces each codon frequency, Relative Synonymous Codons Uses and Relative Adaptiveness of a Codon that can help to calculate the Codon Adaptation Index (CAI) of a gene.
We generate a Graph between RSCU & RAC for better analysis.
Reference:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3547335
USES or Examples
You can use this module in the following ways
use Bio::Tools::CodonOptTable;
my $seqobj = Bio::Tools::CodonOptTable->new(
-seq => 'ATGGGGTGGGCACCATGCTGCTGTCGTGAATTTGGGCACGATGGTGTACGTGCTCGTAGCTAGGGTGGGTGGTTTG',
-id => 'GeneFragment-12',
-accession_number => 'Myseq1',
-alphabet => 'dna',
-is_circular => 1,
-genetic_code => 1,
);
#If you wanna read from file
my $seqobj = Bio::Tools::CodonOptTable->new(
-file => "contig.fasta",
-format => 'Fasta',
-genetic_code => 1,
);
#If you have Accession number and want to get file from NCBI
my $seqobj = Bio::Tools::CodonOptTable->new(
-ncbi_id => "J00522",
-genetic_code => 1,
);
my $myCodons = $seqobj->rscu_rac_table();
if ($myCodons) {
foreach my $each_aa (@$myCodons) {
print "Codon : ", $each_aa->{'codon'}, "\t";
print "Frequency : ", $each_aa->{'frequency'}, "\t";
print "AminoAcid : ", $each_aa->{'aa_name'}, "\t";
print "RSCU Value : ", $each_aa->{'rscu'}, "\t"; #Relative Synonymous Codons Uses
print "RAC Value : ", $each_aa->{'rac'}, "\t"; #Relative Adaptiveness of a Codon
print "\n";
}
}
# To get the prefered codon list based on RSCU & RAC Values
my $prefered_codons = $seqobj->prefered_codon($myCodons);
while ( my ( $amino_acid, $codon ) = each(%$prefered_codons) ) {
print "AminoAcid : $amino_acid \t Codon : $codon\n";
}
# To produce a graph between RSCU & RAC
# Graph output file extension should be GIF, we support GIF only
$seqobj->generate_graph( $myCodons, $outfile_name );
# To Calculate Codon Adaptation Index (CAI)
my $gene_cai = $seqobj->calculate_cai($myCodons);
# To Produce HTML report
# This function will generate HTML report, outfile extension should be .html
$seqobj->generate_report($outfile_name);
INSTALLATION
To install this module, run the following commands:
perl Makefile.PL
make
make test
make install
SUPPORT AND DOCUMENTATION
After installing, you can find documentation for this module with the
perldoc command.
perldoc Bio::Tools::CodonOptTable
You can also look for information at:
RT, CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tools-CodonOptTable
AnnoCPAN, Annotated CPAN documentation
http://annocpan.org/dist/Bio-Tools-CodonOptTable
CPAN Ratings
http://cpanratings.perl.org/d/Bio-Tools-CodonOptTable
Search CPAN
http://search.cpan.org/dist/Bio-Tools-CodonOptTable
COPYRIGHT AND LICENCE
Copyright (C) 2010 Rakesh Kumar Shardiwal
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.